Tag Archives: PLINK


Friday SNPpets

This Friday includes a range of topics, as usual. Interesting assessments of the state of autism genomic architecture–and read the piece on the “ghettoization” of genetic disease after that (Laura Hercher’s tweet). Horizontal gene transfer in cheese bacteria. Traits in crops. CRISPR for insects. Deep time in human DNA, and evolutionary history of tumors. There are so many great things around right now…. Off we go!

SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: SNPexp, correlation between SNPs & gene expression

SNPexp is a nice simple tool that uses PLINK to  calculate the correlation (p-value) between SNPs in a given range of locations in the genome, or alternatively a list of specific SNP rsIDs, and the expression of a gene of interest. It combines the data from these two datasets: the HapMap project and GENEVAR*. It provides a simple web-based interface to allow you to make those calculations and to either download the results in a series of files, or to view the results as a custom track in the UCSC Genome Browser. Today’s tip gives you a quick introduction to using the tool.

*GENEVAR is both a database of  “analysis of gene expression variation in the HapMap samples using genome-wide expression arrays (47294 transcripts) from EBV-transformed lymphoblastoid cell lines from the same 270 HapMap individuals AND a downloadable software tool to allow you to “perform analysis and visualization of associations between sequence variation and gene expression in eQTL studies.” It’s an additional tool that might be of interest and providing for more in-depth analysis.

Quick link to SNPexp: http://app3.titan.uio.no/biotools/tool.php?app=snpexp